| 84 | | === [=#repro Step 4 [for peak-calling experiments with replication]: Identify reproducible peaks] === |
| 85 | | |
| 86 | | For more information about the method, see the main [[https://github.com/nboley/idr | IDR page]]. |
| 87 | | |
| 88 | | Run macs2 (macs version 2, not version 1) to call ChIP-seq peaks (see step 3) |
| 89 | | |
| 90 | | The IDR analysis requires that you call lots of peaks, including all "good" ones (signal) and some bad ones (noise). |
| | 84 | === [=#repro Step 4: Identify reproducible peaks with the IDR method [for peak-calling experiments with replication]] === |
| | 85 | |
| | 86 | You can identify reproducible peaks with idr function, based on the method of [[https://projecteuclid.org/journals/annals-of-applied-statistics/volume-5/issue-3/Measuring-reproducibility-of-high-throughput-experiments/10.1214/11-AOAS466.full | Qunhua Li et al]] and using [[https://github.com/nboley/idr | code from Nathan Boley]]. |
| | 87 | |
| | 88 | Start by running macs2 (macs version 2, not version 1) to call ChIP-seq peaks (see step 3) |
| | 89 | |
| | 90 | The IDR analysis requires that you call lots of peaks, including more than the obvious "good" ones (signal). |
